Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,096,773	C→T	23.5%	A48T (GCC→ACC)	htpX ←	protease HtpX

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,096,773	0	C	T	23.5%	29.6 / 4.3	17	A48T (GCC→ACC)	htpX	protease HtpX
Reads supporting (aligned to +/- strand):  ref base C (5/8);  new base T (2/2);  total (7/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTCGACCGTTTGCAGCAGCCACTGCTCGTGGCGGGTGCGCGGCTGGCTGATGATCTGGGTGCCGGTGGTCATCTTCGCCATCCACTTGGAGATGAACAGCGAAACGAGGGAGCCGGCAAAGCCGAACACGGCGCAGAACACCAGCAGGCTGCTGAGGTTCAGGTCGACCCCGTTGGCGGCCATGAACCCGTTGAAACCGAACAGGCTCAGGGTAATGCTTGCAACCAGCACCACCGCGAGGTTGGTG  >  NC_002947/2096642‑2096888                                                                                                                                    |                                                                                                                    ttCGACCGTTTGCAGCAGCCACTGCTCGTGGCGGGTGCGCGGCTGGCTGATGATCTGGGTGCCGGTGGTCATCTTCGCCATCCACTTGGAGATGAACAGCGAAACGAGGGAGCCGGCAAAGCCGAACACGGCGCAg                                                                                                                 >  1:405332/1‑136 (MQ=255) ttCGACCGTTTGCAGCAGCCACTGCTCGTGGCGGGTGCGCGGCTGGCTGATGATCTGGGTGCCGGTGGTCATCTTCGCCATCCACTTGGAGATGAACAGCGAAACGAGGGAGCCGGCAAAGCCGAACACGGCGCAg                                                                                                                 >  2:368220/1‑136 (MQ=255) ttCGACCGTTTGCAGCAGCCACTGCTCGTGGCGGGTGCGCGGCTGGCTGATGATCTGGGTGCCGGTGGTCATCTTCGCCATCCACTTGGAGATGAACAGCGAAACGAGGGAGCCGGCAAAGCCGAACACGGCGCAg                                                                                                                 >  1:545424/1‑136 (MQ=255)         tttGCAGCAGCCACTGCTCGTGGCGGGTGCGCGGCTGGCTGATGATCTGGGTGCCGGTGGTCATCTTCGCCATCCACTTGGAGATGAACAGCGAAACGAGGGAGCCGGCAAAGCCGAACACGGTGCAGAACACcag                                                                                                         >  2:39558/1‑136 (MQ=255)         tttGCAGCAGCCACTGCTCGTGGCGGGTGCGCGGCTGGCTGATGATCTGGGTGCCGGTGGTCATCTTCGCCATCCACTTGGAGATGAACAGCGAAACGAGGGAGCCGGCAAAGCCGAACACGGTGCAGAACACcag                                                                                                         >  2:36844/1‑136 (MQ=255)               gctgcCACTGCTCGTGGCGGGGTCGCGGCTGGCTGATGATCTGGGTGCCGGTGGTCATCTTCGCCATCCACTTGGAGATGAACAGCGAAACGAGGGAGCCGGCAAAGCCGAACACGGCGCAGAACACCAGCAGgct                                                                                                   <  1:86396/133‑1 (MQ=255)                ctgcCAGTGCTCGTGGGGGGTGCGCGGCTGGCTGTTGATCTGGGTGCCGGTGGTCATCTTCGCCATCCACTTGGAGATGAACAGCGAAACGAGGGAGCCGGCAAAGCCGAACACGGCGCAGAACACCAGCAGgctg                                                                                                  <  2:110365/134‑1 (MQ=255)                                       gcgGCTGGCTGATGATCTGGGTGCCGGTGTTCATCTTCGCCATCCACTTGGAGATGAACAGCGAAACGAGGGAGCCGGCAAAGCCGAACACGGTGCAGAACACCAGCAGGCTGCTGAGGTTCAGGTCGACCCCGtt                                                                           <  1:36844/136‑1 (MQ=255)                                       gcgGCTGGCTGATGATCTGGGTGCCGGTGGTCATCTTCGCCATCCACTTGGAGATGAACAGCGAATCGAGGGAGCCGGCAAAGCCGAACACGGTGCAGAACACCAGCAGGCTGCTGAGGTTCAGGTCGACCCCGtt                                                                           <  1:39558/136‑1 (MQ=255)                                                tgatgaTCTGGGTGCCGGTGGTCATCTTCGCCATCCACTTGGAGATGAACAGCGAAACGAGGGAGCCGGCAAAGCCGAACACGGCGCAGAACACCAGCAGGCTGCTGAGGTTCAGGTCGACCCCGTTGGCGGCCAt                                                                  <  2:545424/136‑1 (MQ=255)                                                               cGGTGGTCATCTTCGCCATCCACTTGGAGATGAACAGCGAAACGAGGGAGCCGGCAAAGCCGAACACGGCGCAGAACACCAGCAGGCTGCTGAGGTTCAGGTCGACCCCGTTGGCGGCCATGAACCCGTTGAAAcc                                                   <  2:130752/136‑1 (MQ=255)                                                               cGGTGGTCATCTTCGCCATCCACTTGGAGATGAACAGCGAAACGAGGGAGCCGGCAAAGCCGAACACGGCGCAGAACACCAGCAGGCTGCTGAGGTTCAGGTCGACCCCGTTGGCGGCCATGAACCCGTTGAAAcc                                                   <  1:261434/136‑1 (MQ=255)                                                                ggtggtCATCTTCGCCATCCACTTGGAGATGAACAGCGAAACGAGGGAGCCGGCAAAGCCGAACACGGCGCAGAACACCAGCAGGCTGCTGAGGTTCAGGTCGACCCCGTTGGCGGCCATGAACCCGTTGAAACCg                                                  <  2:312906/136‑1 (MQ=255)                                                                      cATCTTCGCCATCCACTTGGAGATGAACAGCGAAACGAGGGAGCCGGCAAAGCCGAACACGGCGCAGAACACCAGCAGGCTGCTGAGGTTCAGGTCGACCCCGTTGGCGGCCATGAACCCGTTGAAACCGAACAgg                                            <  1:6642/136‑1 (MQ=255)                                                                                           gaTGAACAGCGAAACGAGGGAGCCGGCAAAGCCGAACACGGCGCAGAACACCAGCAGGCTGCTGAGGTTCAGGTCGACCCCGTTGGCGGCCATGAACCCGTTGAAACCGAACAGGCTCAGGGTAATGCTTGCAAcc                       >  2:506320/1‑136 (MQ=255)                                                                                                       aaCGAGGGAGCCGGCAAAGCCGAACACGGCGCAGAACACCAGCAGGCTGCTGAGGTTCAGGTCGACCCCGTTGGCGGCCATGAACCCGTTGAAACCGAACAGGCTCAGGGTAATGCTTGCAACCAGCACCACcgcg           >  1:451994/1‑136 (MQ=255)                                                                                                                gCCGGCAAAGCCGAACACGGCGCAGAACACCAGCAGGCTGCTGAGGTTCAGGTCGACCCCGTTGGCGGCCATGAACCCGTTGAAACCGAACAGGCTCAGGGTAATGCTTGCAACCAGCACCACCGCGAGGTtggtg  <  2:405332/136‑1 (MQ=255)                                                                                                                                    |                                                                                                                    TTCGACCGTTTGCAGCAGCCACTGCTCGTGGCGGGTGCGCGGCTGGCTGATGATCTGGGTGCCGGTGGTCATCTTCGCCATCCACTTGGAGATGAACAGCGAAACGAGGGAGCCGGCAAAGCCGAACACGGCGCAGAACACCAGCAGGCTGCTGAGGTTCAGGTCGACCCCGTTGGCGGCCATGAACCCGTTGAAACCGAACAGGCTCAGGGTAATGCTTGCAACCAGCACCACCGCGAGGTTGGTG  >  NC_002947/2096642‑2096888

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑